Structural Properties of the Nickel Ions in Urease: Novel Insights Into the Catalytic and Inhibition Mechanisms
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Structural Insights Into Histone Modifying Enzymes
Wayne State University Wayne State University Theses January 2019 Structural Insights Into Histone Modifying Enzymes Shruti Amle Wayne State University, [email protected] Follow this and additional works at: https://digitalcommons.wayne.edu/oa_theses Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Amle, Shruti, "Structural Insights Into Histone Modifying Enzymes" (2019). Wayne State University Theses. 693. https://digitalcommons.wayne.edu/oa_theses/693 This Open Access Embargo is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Theses by an authorized administrator of DigitalCommons@WayneState. STRUCTURAL INSIGHTS INTO HISTONE MODIFYING ENZYMES by SHRUTI AMLE THESIS Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE 2019 MAJOR: BIOCHEMISTRY AND MOLECULAR BIOLOGY Approved By: _________________________________________ Advisor Date _________________________________________ _________________________________________ _________________________________________ i ACKNOWLEDGEMENTS Writing this thesis has been extremely captivating and gratifying. I take this opportunity to express my deep and sincere acknowledgements to the number of people for extending their generous support and unstinted help during my entire study. Firstly, I would like to express my respectful regards and deep sense of gratitude to my advisor, Dr. Zhe Yang. I am extremely honored to study and work under his guidance. His vision, ideals, timely motivation and immense knowledge had a deep influence on my entire journey of this career. Without his understanding and support, it would not have been possible to complete this research successfully. I also owe my special thanks to my committee members: Dr. -
Purification Andsomeproperties of Cytosine Deaminase from Bakers
Agric. Biol. Chem., 53 (5), 1313-1319, 1989 1313 Purification and SomeProperties of Cytosine Deaminase from Bakers' Yeast Tohoru Katsuragi, Toshihiro Sonoda, Kin'ya Matsumoto, Takuo Sakai and Kenzo Tonomura Laboratory of Fermentation Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai-shi, Osaka 591, Japan Received November 24, 1988 Cytosine deaminase (EC 3.5.4.1) was extracted from commercial compressed bakers' yeast and purified to an almost homogeneous state. The enzyme activity was more than 200U/mg of protein, which was several times higher than reported before. The molecular weight was 41,000 by gel permeation. The pi was at pH4.7. 5-Fluorocytosine, 5-methylcytosine, and creatinine were other substrates for the enzyme.An experiment with inhibitors suggested that the enzyme was an SH- enzyme. The enzyme was unstable to heat, with a half-life of about 0.5hr at 37°C. Characteristics of the enzyme, especially its substrate specificity, were compared with those reported earlier for other cytosine deaminases from bacteria and a mold. Local chemotherapy of cancer with the com- (5MC), a 5-substituted cytosine.4) 5FC, an- bined use of 5-fluorocytosine (5FC) given oral- other 5-substituted cytosine, is deaminated to ly and a cytosine deaminase capsule implant- 5FU in Saccharomyces cerevisiae.5) So, cy- ed locally may be possible.1} However, al- tosine deaminase of bakers' yeast should con- though this approach is successful in animal vert 5FCto 5FU, and could be used in place of experiments,1'2) there are problems when we E. coli cytosine deaminase. Although the yeast use the enzyme from Escherichia coli,3) which enzyme is unstable to heat (at 37.5°C),4) which is thermostable,1'3) and which can deaminate would prevent its use in long-term therapy in 5FC to 5-fluorouracil (5FU).1>3) First, it is the body, it might be stabilized by immobili- difficult to culture the bacteria on a large scale zation or other techniques. -
Molecular Basis of NDT-Mediated Activation of Nucleoside-Based Prodrugs and Application in Suicide Gene Therapy
biomolecules Article Molecular Basis of NDT-Mediated Activation of Nucleoside-Based Prodrugs and Application in Suicide Gene Therapy Javier Acosta 1,† , Elena Pérez 1,†, Pedro A. Sánchez-Murcia 2, Cristina Fillat 3,4 and Jesús Fernández-Lucas 2,5,* 1 Applied Biotechnology Group, European University of Madrid, c/ Tajo s/n, Villaviciosa de Odón, 28670 Madrid, Spain; [email protected] (J.A.); [email protected] (E.P.) 2 Division of Physiological Chemistry, Otto-Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria; [email protected] 3 Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; cfi[email protected] 4 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain 5 Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66 Barranquilla, Colombia * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Herein we report the first proof for the application of type II 20-deoxyribosyltransferase from Lactobacillus delbrueckii (LdNDT) in suicide gene therapy for cancer treatment. To this end, we first confirm the hydrolytic ability of LdNDT over the nucleoside-based prodrugs 20-deoxy-5- fluorouridine (dFUrd), 20-deoxy-2-fluoroadenosine (dFAdo), and 20-deoxy-6-methylpurine riboside (d6MetPRib). Such activity was significantly increased (up to 30-fold) in the presence of an acceptor nucleobase. To shed light on the strong nucleobase dependence for enzymatic activity, different molecular dynamics simulations were carried out. Finally, as a proof of concept, we tested the LdNDT/dFAdo system in human cervical cancer (HeLa) cells. -
Harnessing the Power of Bacteria in Advancing Cancer Treatment
International Journal of Molecular Sciences Review Microbes as Medicines: Harnessing the Power of Bacteria in Advancing Cancer Treatment Shruti S. Sawant, Suyash M. Patil, Vivek Gupta and Nitesh K. Kunda * Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Jamaica, NY 11439, USA; [email protected] (S.S.S.); [email protected] (S.M.P.); [email protected] (V.G.) * Correspondence: [email protected]; Tel.: +1-718-990-1632 Received: 20 September 2020; Accepted: 11 October 2020; Published: 14 October 2020 Abstract: Conventional anti-cancer therapy involves the use of chemical chemotherapeutics and radiation and are often non-specific in action. The development of drug resistance and the inability of the drug to penetrate the tumor cells has been a major pitfall in current treatment. This has led to the investigation of alternative anti-tumor therapeutics possessing greater specificity and efficacy. There is a significant interest in exploring the use of microbes as potential anti-cancer medicines. The inherent tropism of the bacteria for hypoxic tumor environment and its ability to be genetically engineered as a vector for gene and drug therapy has led to the development of bacteria as a potential weapon against cancer. In this review, we will introduce bacterial anti-cancer therapy with an emphasis on the various mechanisms involved in tumor targeting and tumor suppression. The bacteriotherapy approaches in conjunction with the conventional cancer therapy can be effective in designing novel cancer therapies. We focus on the current progress achieved in bacterial cancer therapies that show potential in advancing existing cancer treatment options and help attain positive clinical outcomes with minimal systemic side-effects. -
A Highly Efficient Non-Viral Process for Programming Mesenchymal Stem
www.nature.com/scientificreports OPEN A highly efcient non‑viral process for programming mesenchymal stem cells for gene directed enzyme prodrug cancer therapy Yoon Khei Ho*, Jun Yung Woo, Geraldine Xue En Tu, Lih‑Wen Deng & Heng‑Phon Too* Mesenchymal stem cells (MSCs) driven gene‑directed enzyme prodrug therapy has emerged as a potential strategy for cancer treatment. The tumour‑nesting properties of MSCs enable these vehicles to target tumours and metastases with efective therapies. A crucial step in engineering MSCs is the delivery of genetic material with low toxicity and high efciency. Due to the low efciency of current transfection methods, viral vectors are used widely to modify MSCs in preclinical and clinical studies. We show, for the frst time, the high transfection efciency (> 80%) of human adipose tissue derived‑ MSCs (AT‑MSCs) using a cost‑efective and of‑the‑shelf Polyethylenimine, in the presence of histone deacetylase 6 inhibitor and fusogenic lipids. Notably, the phenotypes of MSCs remained unchanged post‑modifcation. AT‑MSCs engineered with a fused transgene, yeast cytosine deaminase::uracil phosphoribosyltransferase (CDy::UPRT) displayed potent cytotoxic efects against breast, glioma, gastric cancer cells in vitro. The efciency of eliminating gastric cell lines were efective even when using 7‑day post‑transfected AT‑MSCs, indicative of the sustained expression and function of the therapeutic gene. In addition, signifcant inhibition of temozolomide resistant glioma tumour growth in vivo was observed with a single dose -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
Expression of the Prodrug-Activating Enzyme DT-Diaphorase Via Ad5
Cancer Gene Therapy (2002) 9, 209–217 D 2002 Nature Publishing Group All rights reserved 0929-1903/02 $25.00 www.nature.com/cgt Expression of the prodrug-activating enzyme DT-diaphorase via Ad5 delivery to human colon carcinoma cells in vitro Veet Misra, Henry J Klamut, and AM Rauth Division of Experimental Therapeutics, Ontario Cancer Institute, Toronto, Ontario, Canada; and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. Intratumoral injection of recombinant adenoviral type 5 (Ad5) vectors that carry prodrug-activating enzymes like DT-diaphorase (DTD) could be used to selectively target tumor cells for chemotherapy. To demonstrate the feasibility of this approach, Ad5 vectors were constructed, which express human DTD minigenes for both wild-type and mutant (C-to-T change in nucleotide 609 in DTD cDNA) DTD under the control of the cytomegalovirus (CMV) promoter. HT29 human colon carcinoma cells express wild-type DTD, whereas BE human colon carcinoma cells express mutant DTD, have low to undetectable DTD activity, and are 4- to 6-fold more resistant to mitomycin C (MMC) than HT29 cells. A test of the ability of Ad5 to infect these cells (using a -galactosidase CMV- driven minigene) indicated that 90–100% of BE cells were infected at a multiplicity of infection (MOI) of 100, whereas only 15– 40% of HT29 cells were infected at this MOI. Infection of BE cells in vitro with recombinant Ad5 carrying a minigene for wild-type DTD at MOIs of 3–100 resulted in a progressive increase in DTD activity and a maximal 8-fold increase in sensitivity to MMC as measured by a colony-forming assay. -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle. -
RECOMBINANT DNA ADVISORY COMMITTEE Minutes of Meeting December 15-16, 1997
RECOMBINANT DNA ADVISORY COMMITTEE Minutes of Meeting December 15-16, 1997 U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES Public Health Service National Institutes of Health TABLE OF CONTENTS I. Call to Order and Opening Remarks/Mickelson II. RAC Forum on New Technologies III. Food and Drug Administration (FDA) Presentation: Discussion of the Risks of Gonadal Distribution and Inadvertent Germ Line Integration in Patients Receiving Direct Administration of Gene Therapy Vectors IV. Call to Order/Mickelson V. Minutes of the September 12, 1997, Meeting/Ando, Greenblatt VI. Update on Data Management/Greenblatt VII. Amendment to Institutional Biosafety Committee Approvals of Experiments Involving Transgenic Rodents Under Section III of the NIH Guidelines/Aguilar-Cordova VIII. Amendment to Appendix K, Physical Containment for Large Scale Uses of Organisms Containing Recombinant DNA Molecules/McGarrity IX. Amendment to Section III-D-6, Experiments Involving More than 10 Liters of Culture/Knazek X. Human Gene Transfer Protocol #9708-209 entitled: Systemic and Respiratory Immune Response to Administration of an Adenovirus Type 5 Gene Transfer Vector (AdGVCD.10)/Harvey, Crystal XI. Human Gene Transfer Protocol #9711-221 entitled: Phase I Study of Direct Administration of a Replication-Deficient Adenovirus Vector (AdGVVEGF121.10) Containing the VEGF121 cDNA to the Ischemic Myocardium of Individuals with Life Threatening Diffuse Coronary Artery Disease/Crystal XII. Amendment to Appendix M-I, Submission Requirements--Human Gene Transfer Experiments Regarding the Timing of Institutional Biosafety Committee and Institutional Review Board Page 1 Approvals/Markert XIII. Human Gene Transfer Protocol #9708-211 entitled: Gene Therapy for Canavan Disease/Seashore XIV. Amendment to Appendix M-I, Submission Requirements--Human Gene Transfer Experiments Regarding Deadline Submission for RAC Review/McIvor XV. -
Annotating Enzymes of Unknown Function: N
Biochemistry 2006, 45, 1997-2005 1997 Annotating Enzymes of Unknown Function: N-Formimino-L-glutamate Deiminase Is a Member of the Amidohydrolase Superfamily† Ricardo Martı´-Arbona, Chengfu Xu, Sondra Steele, Amanda Weeks, Gabriel F. Kuty, Clara M. Seibert, and Frank M. Raushel* Department of Chemistry, P.O. Box 30012, Texas A&M UniVersity, College Station, Texas 77842-3012 ReceiVed December 13, 2005; ReVised Manuscript ReceiVed January 2, 2006 ABSTRACT: The functional assignment of enzymes that catalyze unknown chemical transformations is a difficult problem. The protein Pa5106 from Pseudomonas aeruginosa has been identified as a member of the amidohydrolase superfamily by a comprehensive amino acid sequence comparison with structurally authenticated members of this superfamily. The function of Pa5106 has been annotated as a probable chlorohydrolase or cytosine deaminase. A close examination of the genomic content of P. aeruginosa reveals that the gene for this protein is in close proximity to genes included in the histidine degradation pathway. The first three steps for the degradation of histidine include the action of HutH, HutU, and HutI to convert L-histidine to N-formimino-L-glutamate. The degradation of N-formimino-L-glutamate to L-glutamate can occur by three different pathways. Three proteins in P. aeruginosa have been identified that catalyze two of the three possible pathways for the degradation of N-formimino-L-glutamate. The protein Pa5106 was shown to catalyze the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate, while Pa5091 catalyzed the hydrolysis of N-formyl-L-glutamate to formate and L-glutamate. The protein Pa3175 is dislocated from the hut operon and was shown to catalyze the hydrolysis of N-formimino-L-glutamate to formamide and L-glutamate. -
PURINE SALVAGE in HELICOBACTER PYLORI by ERICA FRANCESCA MILLER (Under the Direction of Robert J. Maier) ABSTRACT Purines Are Es
PURINE SALVAGE IN HELICOBACTER PYLORI by ERICA FRANCESCA MILLER (Under the Direction of Robert J. Maier) ABSTRACT Purines are essential for all living cells. This fact is reflected in the high degree of pathway conservation for purine metabolism across all domains of life. The availability of purines within a mammalian host is thought to be a limiting factor for infection, as demonstrated by the importance of purine synthesis and salvage genes among many bacterial pathogens. Helicobacter pylori, a primary causative agent of peptic ulcers and gastric cancers, colonizes a niche that is otherwise uninhabited by bacteria: the surface of the human gastric epithelium. Despite many studies over the past 30 years that have addressed virulence mechanisms such as acid resistance, little knowledge exists regarding this organism’s purine metabolism. To fill this gap in knowledge, we asked whether H. pylori can carry out de novo purine biosynthesis, and whether its purine salvage network is complete. Based on genomic data from the fully sequenced H. pylori genomes, we combined mutant analysis with physiological studies to determine that H. pylori, by necessity, must acquire purines from its human host. Furthermore, we found the purine salvage network to be complete, allowing this organism to use any single purine nucleobase or nucleoside for growth. In the process of elucidating these pathways, we discovered a nucleoside transporter in H. pylori that, in contrast to the biochemically- characterized homolog NupC, aids in uptake of purine rather than pyrimidine nucleosides into the cell. Lastly, we investigated an apparent pathway gap in the genome annotation—that of adenine degradation—and in doing so uncovered a new family of adenosine deaminase that lacks sequence homology with all other adenosine deaminases studied to date. -
Global Gene Expression in Escherichia Coli
Ranjith et al. Gut Pathog (2017) 9:15 DOI 10.1186/s13099-017-0164-2 Gut Pathogens RESEARCH Open Access Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm Konduri Ranjith1,3, Kotakonda Arunasri1, Gundlapally Sathyanarayana Reddy2, HariKrishna Adicherla2, Savitri Sharma1 and Sisinthy Shivaji1* Abstract Background: Escherichia coli, the gastrointestinal commensal, is also known to cause ocular infections such as con- junctivitis, keratitis and endophthalmitis. These infections are normally resolved by topical application of an appropri- ate antibiotic. But, at times these E. coli are resistant to the antibiotic and this could be due to formation of a biofilm. In this study ocular E. coli from patients with conjunctivitis, keratitis or endophthalmitis were screened for their antibiotic susceptibility and biofilm formation potential. In addition DNA-microarray analysis was done to identify genes that are involved in biofilm formation and antibiotic resistance. Results: Out of 12 ocular E. coli isolated from patients ten isolates were resistant to one or more of the nine antibi- otics tested and majority of the isolates were positive for biofilm formation. In E. coli L-1216/2010, the best biofilm forming isolate, biofilm formation was confirmed by scanning electron microscopy. Confocal laser scanning micro- scopic studies indicated that the thickness of the biofilm increased up to 72 h of growth. Further, in the biofilm phase, E. coli L-1216/2010 was 100 times more resistant to the eight antibiotics tested compared to planktonic phase. DNA microarray analysis indicated that in biofilm forming E.